The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species

TitleThe Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species
Publication TypeJournal Article
Year of Publication2019
AuthorsFaber-Hammond, JJ, Bezault, E, Lunt, DH, Joyce, DA, Renn, SCP
JournalGenome Biology and Evolution
Pagination2856 - 2874
Date PublishedJan-10-2019
Keywordsadaptive radiation, cichlid, copy number variation, gene duplication, genomic architecture

The initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has the potential to generate substantial molecular substrate for the origin of evolutionary novelty. We use array-based comparative heterologous genomic hybridization to identify copy number variation events (CNVEs) for 168 samples representing 53 cichlid species including the 5 species for which full genome sequence is available. We identify an average of 50-100 CNVEs per individual. For those species represented by multiple samples, we identify 150-200 total CNVEs suggesting a substantial amount of intraspecific variation. For these species, only ∼10% of the detected CNVEs are fixed. Hierarchical clustering of species according to CNVE data recapitulates phylogenetic relationships fairly well at both the tribe and radiation level. Although CNVEs are detected on all linkage groups, they tend to cluster in "hotspots" and are likely to contain and be flanked by transposable elements. Furthermore, we show that CNVEs impact functional categories of genes with potential roles in adaptive phenotypes that could reasonably promote divergence and speciation in the cichlid clade. These data contribute to a more complete understanding of the molecular basis for adaptive natural selection, speciation, and evolutionary radiation.

Author Address

1- Department of Biology, Reed College, Portland OR 97202.

2- BOREA Research Unit, MNHN, CNRS 7208, Sorbonne Université, IRD 207, UCN, UA, Paris, France.

3- Department of Biological and Marine Sciences, University of Hull, Hull Kingston-Upon-Hull, United Kingdom.

PubMed ID31504491
PubMed Central IDPMC6795240
Catégorie HCERES
ACL - Peer-reviewed articles
Publication coopération et recherche SUD